Diagnostic evaluation of antibody responses to commonly recognized prostate cancer-associated antigens

The present invention relates to a plurality of antigens that together form a panel of immunoreactive molecules suitable for identifying candidates for prostate cancer examination. Methods for identifying antibodies indicative of a pre-malignant or malignant prostate are disclosed. Further disclosed are kits that can be used to practice the above methods.

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Description
CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. application Ser. No. 13/088,594, filed Apr. 18, 2011, now abandoned, which claims the benefit of U.S. Provisional Patent Application No. 61/324,953, filed Apr. 16, 2010, each of which is incorporated herein by reference as if set forth in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under RR016489 awarded by the National Institutes of Health. The government has certain rights in the invention.

SEQUENCE LISTING

A sequence listing is submitted in PDF and text formats on one Compact Disc-Read Only Memory (CD-ROM), in duplicate, and is incorporated herein by reference. “Copy 1” of the CD-ROM contains Seq List 960296_01933_ST25.PDF, created Dec. 23, 2015, 1620 KB and Seq List 960296_01933_ST25.TXT, created Dec. 23, 2015, 2695 KB. “Copy 2” of the CD-ROM contains Seq List 960296_01933_ST25.PDF, created Dec. 23, 2015, 1620 KB and Seq List 960296_01933_ST25.TXT, created Dec. 23, 2015, 2695 KB.

BACKGROUND

Prostate cancer is prevalent worldwide. Men living in the United States have approximately a 1 in 6 chance of being diagnosed with prostate cancer at some point during their lifetime, and approximately a 1 in 50 chance of dying from prostate cancer (Jemal et al., CA Cancer J. Clin. 59:225-249 (2009), incorporated herein by reference as if set forth in its entirety). The number of men afflicted with prostate cancer is increasing rapidly as the population of males over the age of 50 grows. Thus, strategies for detecting prostate cancer in its early stages are urgently needed.

Conventional prostate cancer screening methods, including digital rectal examination, transrectal ultrasound, and prostate specific antigen (PSA) testing, lack sensitivity and specificity. Elements of PSA screening are controversial: practitioners disagree on the best age for screening, how to interpret elevated PSA values, and how to identify prostate cancers in patients with low serum PSA values. There are also concerns that PSA screening may lead to unnecessary interventions that do not affect long-term outcome and survival (Greene et al., J Urol 182:2232-2241 (2009), incorporated herein by reference as if set forth in its entirety). To overcome the disadvantages of prostate cancer screening methods, researchers have attempted to identify antigens produced by tumor cells that can be utilized as prostate cancer markers. Serum-based screening methods have allowed for rapid identification of many tumor antigens in individuals with many different tumor types (Sahin et al., Proc. Nat. Acad. Sci. 92:11810-11813(1995), incorporated herein by reference as if set forth in its entirety). In fact, serum screening has been so successful that literally hundreds of cancer-associated antigenic proteins have been identified.

Serological identification of antigens by recombinant expression cloning (SEREX) has been used to prioritize potential vaccine targets for prostate cancer. Immunologically recognized proteins of the prostate have been identified by screening sera from: i) individuals with prostate cancer (Dunphy et al., Update Canc. Ther. 22:273-284 (2006); Fossa et al., Br. J. Cancer 83:743-749 (2000); Mooney et al., Int. J. Urol. 13:211-217 (2006)); ii) prostate cancer individuals treated with immune-active therapies (Dunphy et al., J. Immunother. 28:268-275 (2005)); and iii) prostate cancer individuals treated with standard androgen deprivation therapy (Morse and McNeel, Hum. Immunol. 71:496-504 (2010)); each of the foregoing references are herein incorporated by reference as if set forth in their entirety). Sera from individuals with prostate cancer were also used to directly screen a testis tissue cDNA expression library and a panel of defined cancer-testis antigens aberrantly expressed in solid tumors of different histologic types (Hoeppner et al., Cancer Immun. 6:1-7 (2006); Dubovsky and McNeel, Prostate 67:1781-1790 (2007), each incorporated herein by reference as if set forth in its entirety).

Chronic inflammation has been implicated in lung and colon cancers and might similarly promote the development of prostate cancers (Palapattu et al., Carcinogenesis 26:1170-1181 (2005); Narayanan et al., Prostate 69:133-141 (2009); McDowell et al., Prostate 70:377-389 (2010); Dennis et al., Urology 60:78-83 (2002); each incorporated herein by reference as if set forth in its entirety). Tumor-infiltrating lymphocytes are observed in prostate tumor specimens, and chronic inflammatory cells (e.g., lymphocytes and mononuclear cells) are observed adjacent to the earliest premalignant lesions of the prostate (De Marzo et al., Am. J. Pathol. 155:1985-1992 (1999) incorporated by reference herein as if set forth in its entirety). In rodents, chronic prostatitis appears to promote the development of prostate tumors (Gilardoni et al., J. Exp. Clin. Cancer Res. 18:493-504 (1999), incorporated by reference herein as if set forth in its entirety). Human prostate-infiltrating lymphocytes obtained at the time of surgery are oligoclonal suggesting that these lymphocytes recognize tissue-specific antigens (Mercader et al., Proc. Nat. Acad. Sci. 98:14565-14570 (2001); Sfanos et al., Prostate 69:1694-1703 (2009); each incorporated herein by reference as if set forth in its entirety).

While a number of antigens associated with prostate cancer have been identified, it has not yet been determined which of these antigens are predictive of a malignant or premalignant prostate. This is at least in part due to the variation in antibody-antigen profiles of individuals; not every antigen associated with prostate cancer or prostatitis is expressed in every affected individual and not every expressed antigen elicits an immune response in every affected individual. As such, no single antigen can serve as a reliable indicator of prostate cancer or prostatitis. The high level of variation of immunoresponsiveness among individuals has made it difficult to translate antigens associated with prostate cancer into tools useful for predicting prostate cancer, or predicting an increased risk of developing prostate cancer, in populations of men, wherein populations are defined as groups with or without a particular disease or disease stage. Screening men for all antigens that have been associated with prostate cancer is cost-prohibitive and impractical. Thus, there is a need in the art to identify a subset of antigens specific to antibodies associated with pre-malignant and malignant prostate tissue for identifying candidate individuals warranting further prostate examination.

BRIEF SUMMARY OF THE INVENTION

The present invention is broadly summarized as relating to a plurality of antigens that together form a set or panel of immunoreactive molecules suitable for identifying candidates for prostate cancer examination. Many cancer detection efforts rely on detecting, with varying degrees of specificity and sensitivity, cancer-associated antigens produced by tumor cells. In contrast, the present invention relies on detecting immunoresponses to tissue-associated antigens. The present invention contemplates using a plurality of these antigens to identify antibodies indicative of a pre-malignant or malignant prostate. As used herein, an “antigen” means a substance that when introduced into an animal stimulates the production of an antibody. An antigen can also be a substance produced by the body, wherein an immune response has been, or can be, elicited to that antigen. As used herein, an “antibody,” is a specialized molecule that can specifically bind the antigen that triggered its production.

In a first aspect, the invention is summarized as an antigen panel for identifying immunoreactivity associated with a premalignant or malignant prostate, the panel comprising a plurality of antigens. As used herein, “immunoreactivity” refers to an animal's immune response to a particular antigen or antigens. One or more of the antigens may be previously known and identified as being recognized by antibodies in individuals having prostate cancer and/or prostatitis. In some embodiments of the first aspect, the panel elicits an immune response in at least about 33% of men with prostate cancer or prostatitis. In other embodiments of the first aspect, 9% of individuals with prostatitis or prostate cancer exhibit an immune response to at least three of the antigens in the panel. As use herein, “about” means within 5% of a stated range.

In some embodiments of the first aspect, the plurality of antigens in the antigen panel is selected from the group consisting of PRO1, PRO2, PRO3, PRO4, PRO5, PRO6, PRO7, PRO8, PRO9, PRO10, PRO11, PRO12, PRO13, PRO14, PRO15, PRO16, PRO17, PRO18, PRO19, PRO20, PRO21, PRO22, PRO23, PRO24, PRO25, PRO26, PRO27, PRO28, PRO29, PRO30, PRO31, PRO32, PRO33, PRO34, PRO35, PRO36, PRO37, PRO38, PRO39, PRO40, PRO41, CTA1, CTA2, CTA3, CTA4, CTA5, CTA6, CTA7, CTA5, CTA9, CTA10, CTA11, CTA12, CTA13, CTA14, CTA15, CTA16, CTA17, CTA18, CTA19, CTA20, CTA21, CTA22, CTA23, CTA24, CTA25, CTA26, CTA27, CTA28, CTA29, PCA1, PCA2, PCA3, PCA4, PCA5, PCA6, PCA7, PCA8, PCA9, PCA10, PCA11, PCA12, PCA13, PCA14, PCA15, PCA16, PCA17, PCA18, PCA19, PCA20, PCA21, PCA22, PCA23, PCA24, PCA25, PCA26, PCA27, PCA28, PCA29, PCA30, ADT1, ADT2, ADT3, ADT4, ADT5, ADT6, ADT7, ADT8, ADT9, ADT10, ADT11, ADT12, ADT13, ADT14, ADT15, ADT16, ADT17, ADT18, ADT19, ADT20, ADT21, ADT22, ADT23, ADT24, ADT25, ADT26, ADT27, and ADT28.

In another embodiment of the first aspect, the plurality of antigens in the panel includes ADT14, CTA3, CTA23, PCA6, PCA8, PCA10, PCA16, PRO5, PRO10, PRO12, PRO17, PRO18, PRO19, PRO20, PRO24, PRO25, PRO35, CTA27, PCA21, PRO40, PCA2, PRO34, and PRO32.

In a second aspect, the invention relates to a method for identifying human or non-human animals as candidates for prostate cancer examination. The method includes the steps of contacting an antigen panel as above with a sample containing at least one antibody specific to at least one antigen of the panel, and observing evidence of immunocomplex formation between at least one antibody from the sample and at least one antigen of the panel. As used herein, “immunocomplex” refers to a complex formed between an antibody and the antigen specifically recognized by the antibody. An individual is identified as a candidate if at least one immunocomplex forms between an antibody from the sample and an antigen in the panel. Samples appropriate for use in the method include, but are not limited to, tissues, cells, and bodily fluids, including blood.

In a third aspect, the present invention relates to a kit comprising an antibody detection panel. The kit comprises an antigen panel containing a plurality of antigens as disclosed herein optionally provided in a carrier or medium.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although suitable materials and methods for the practice or testing of the present invention are described below, other known materials and methods similar or equivalent to those described herein can be used.

Other objectives, advantages and features of the present invention will become apparent from the following specification taken in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

FIG. 1: illustrates high-throughput immunoblot analysis.

FIGS. 2A-2H: illustrate the mean relative density scores for healthy male control blood donors (n=25, open circles) and men with castrate-resistant prostate cancer (n=25, closed circles). Asterisks denote significantly higher median reactivity for the cancer population compared to the control population.

FIGS. 3A-3F illustrate immunoreactivity of individuals with early and late stages of prostate cancer. FIG. 3A shows a heatmap analysis of the relative immunoreactivity for individual antigens indicated by spot color intensity (immunoreactive: white; intermediate: grey; not immunoreactive: black). FIGS. 3B-F illustrates a subset analysis for 23 antigens with the highest positive likelihood ratio values.

FIGS. 4A-4B illustrate the proportion and standard error of subjects in each population recognizing at least one (FIG. 4A) or at least three (FIG. 4B) of the antigens identified in Table II. Asterisks denote higher frequency compared to control population.

FIG. 5: shows a heatmap of the immunoreactivity for individual antigens among sera samples from male patients with non-prostate tumors. A white spot indicates a positive score.

 DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

The present invention generally relates to a novel panel of a plurality of antigens for identifying immunoresponses associated with a premalignant or malignant prostate. As used herein, a “set” or a “panel” refers to a group of antigens associated with a premalignant or malignant prostate. As used herein, “immunoresponse” means the occurrence of a binding reaction between an antibody specific to an antigen and that antigen. As used herein, a premalignant prostate means a prostate characterized by tissue that is not yet malignant, but is poised to become malignant as evidenced by, for example, chronic inflammation or other conditions that can alter cell proliferation and/or cell death. Skilled artisans are familiar with conditions that are associated with changes in cell proliferation and conditions that are associated with changes in cell death. As used herein a malignant prostate refers to a prostate containing tumor-forming prostate epithelial cells.

In some embodiments, one or more of the antigens of the panel is associated with premalignant inflammation of the prostate. As used herein, “premalignant inflammation” means inflammation, the presence of which indicates an increase in an individual's risk for developing a malignant state or condition. Advantageously, the panel includes a plurality of antigens that make the panel more likely to detect immunoreactivity when exposed to antibody-containing samples compared to using a single antigen alone. In some preferred embodiments, antigens having higher specificity for prostate cancer are included in the panel, wherein relative specificity is based on receiver operating curve analysis. In other preferred embodiments, antigens with a positive likelihood ratio greater than 4 (sensitivity/(1−specificity)) are included in the panel. Sensitivity and specificity are based on immunoreactivity of a population of subjects with prostate disease relative to a control population. As used herein, “sensitivity” of an antigen refers to the proportion of positive subjects (i.e., subjects with prostate cancer or prostatitis) identified as positive by presence of an immunoresponse to a particular antigen in an assay. As used herein, “specificity” of an antigen refers to the proportion of negative subjects (i.e., control subjects without prostate cancer or prostatitis) identified as negative by absence of an immunoresponse to a particular antigen in an assay. The likelihood ratio used to rank antigens is a statistical model used to express how many times more likely a dataset is to fit one statistical model rather than another. For example, an antigen having a likelihood ratio of 4 is 4 times more likely to elicit an immunoresponse in a subject having prostatitis or prostate cancer relative to a patient lacking prostatitis or prostate cancer. An antigen can be a natural or synthetic protein or fragment thereof, polysaccharide, or nucleic acid. Skilled artisans know that antigens can induce an immune response and elicit antibody formation. Antibodies can be molecules synthesized in response to the presence of a foreign substance, wherein each antibody has specific affinity for the foreign material that stimulated its synthesis. The specific affinity of an antibody need not be for the entire molecular antigen, but for a particular site on it called the epitope (Kindt et al., Kuby Immunology, 6th Edition 574 pps, (2006), incorporated herein by reference as if set forth in its entirety). Antibodies can be, for example, a natural or synthetic protein or fragment thereof, or nucleic acids (e.g., aptamers) with protein-binding or other antigen-binding characteristics. Antibodies can be produced in response to antigenic stimuli including, but not limited to, exposure to foreign proteins, microorganisms, and toxins. When the panel is contacted with a sample containing at least one antibody specific to an antigen in the panel, an immunocomplex forms between the antigen and the antibody specific for the antigen. One of ordinary skill in the art can assess antigen-antibody imunocomplex formation by techniques commonly used in the art. Examples of suitable techniques to assess immunocomplex formation include phage immunoblot, ELISA, and radioimmunoassay. See, e.g., (Dubovsky et al., J. Immunother. 30:675-683 (2007), incorporated herein by reference as if set forth in its entirety). Samples suitable for use with the method include tissues, cells, and bodily fluids. Preferably, the sample is serum.

In a preferred embodiment, at least about 38% of individuals who have prostate cancer and at least about 33% of individuals who have prostatitis are immunoreactive to at least one antigen of the panel. In another preferred embodiment, at least about 10% of individuals who have prostate cancer and at least about 9% of individuals who have prostatitis are immunoreactive to at least three antigens of the panel. In still another preferred embodiment, antigens of the panel are selected based on their capacity in aggregate to elicit an immune response in at least about 33% of individuals with prostatitis or prostate cancer.

Prostate cancer-relevant cancer-testis antigens (CTA) normally expressed only in MHC class I-deficient germ cells but aberrantly expressed in solid tumors of various histologic types, are suitable for use in the panel. Suitable CTA antigens include, but are not limited to, CTA1, CTA2, CTA3, CTA4, CTA5, CTA6, CTA7, CTA5, CTA9, CTA10, CTA11, CTA12, CTA13, CTA14, CTA15, CTA16, CTA17, CTA18, CTA19, CTA20, CTA21, CTA22, CTA23, CTA24, CTA25, CTA26, CTA27, CTA28, and CTA29. Antigens identified in prostate cancer individuals treated with androgen deprivation therapy (ADT) are also suitable for use in this panel. Suitable ADT antigens include, but are not limited to, ADT1, ADT2, ADT3, ADT4, ADT5, ADT6, ADT7, ADT8, ADT9, ADT10, ADT11, ADT12, ADT13, ADT14, ADT15, ADT16, ADT17, ADT18, ADT19, ADT20, ADT21, ADT22, ADT23, ADT24, ADT25, ADT26, ADT27, and ADT28. Antigens identified in prostate cancer individuals treated with non-ADT prostate cancer therapies (PCA) are also suitable for use in this panel. Suitable PCA antigens include but are not limited to, PCA1, PCA2, PCA3, PCA4, PCA5, PCA6, PCA7, PCA8, PCA9, PCA10, PCA11, PCA12, PCA13, PCA14, PCA15, PCA16, PCA17, PCA18, PCA19, PCA20, PCA21, PCA22, PCA23, PCA24, PCA25, PCA26, PCA27, PCA28, PCA29, and PCA30. Alternatively, antigens identified in subjects with chronic prostatitis (PRO) are suitable for use in this panel. Suitable PRO antigens include, but are not limited to, PRO1, PRO2, PRO3, PRO4, PRO5, PRO6, PRO7, PRO5, PRO9, PRO10, PROM PRO12, PRO13, PRO14, PRO15, PRO16, PRO17, PRO18, PRO19, PRO20, PRO21, PRO22, PRO23, PRO24, PRO25, PRO26, PRO27, PRO28, PRO29, PRO30, PRO31, PRO32, PRO33, PRO34, PRO35, PRO36, PRO37, PRO38, PRO39, PRO40, and PRO41. Exemplary conditions for preparing antigens having epitopes specifically recognized by antibodies specific to the epitopes, are well-known by those of ordinary skill in the art.

In a preferred embodiment, the panel includes ADT14, CTA3, CTA23, PCA6, PCA8, PCA10, PCA16, PRO5, PRO10, PRO12, PRO17, PRO18, PRO19, PRO20, PRO24, PRO25, PRO35, CTA27, PCA21, PRO40, PCA2, PRO34, and PRO32. Omitting one or more of these antigens from the panel might affect the panel's sensitivity. Similarly, adding one or more antigen to this panel might affect the panel's sensitivity. However, a skilled artisan understands that increasing or decreasing the number of antigens in this preferred panel might still provide an acceptable panel of antigens for identifying candidates for further prostate cancer examination.

In another preferred embodiment, the panel includes antigens that have a high likelihood of eliciting immunoresponses in subjects who are candidates for further prostate cancer examination, relative to subjects who are not candidates for further prostate examination, as measured by positive likelihood ratio. In some of these preferred embodiments, antigens of the panel have a positive likelihood ratio of at least 4 (sensitivity/(1−specificity).

In another embodiment, the present invention provides a method for identifying individuals as candidates for further prostate cancer examination. In the method, a panel is contacted with a sample containing one or more antibodies under conditions suitable for antigen-antibody immunocomplex formation. The skilled artisan knows exemplary conditions to allow high-affinity antigen-antibody binding (e.g., Dubrovsky et al., 2007 supra). In the method, presence of an immunocomplex indicates that the individual from whom the sample was obtained is a candidate for further prostate cancer examination.

The disclosed methods can be performed in a single or multi-well format in which each one of the plurality of antigens is placed in a separate well of a multi-well assay plate or, alternatively, in a single container format in which the entire panel of antigens is placed in a single well. The method may be performed in a qualitative format to detect the presence or absence of immunocomplexes, or in a quantitative format to provide a quantitative measurement of the antibodies in a sample. Exemplary conditions used to assay antigens of the inventive panel are well-known by those of ordinary skill in the art.

In another embodiment, the antigen panel can be provided as part of a kit containing a carrier or medium suitable for antigen storage.

The invention will be more fully understood upon consideration of the following non-limiting Examples.

EXAMPLES Example 1: Diagnostic Evaluation of Antibody Responses to Prostate Cancer-Associated Antigens

Multiple antigens were evaluated to identify a subset of immunoreactive antigens in humans with prostate disease. IgG responses were evaluated in subjects with prostate cancer, chronic prostatitis, and in men without prostate disease using phage immunoblot methodology. Results indicated that subjects with prostate cancer or prostatitis have antibodies specific for multiple common antigens: of 128 proteins tested, a subset containing 23 proteins was identified to which antibodies were detected in 38% of subjects with prostate cancer and 33% subjects with prostatitis versus 6% of controls. These results suggest an association between inflammatory conditions of the prostate and prostate cancer, and suggest that antibody responses to a panel of commonly-recognized prostate antigens can be used to identify subjects at risk for prostate cancer.

Materials and Methods

High Throughput Immunoblot (HTI):

Phage immunoblot analysis was performed essentially as described by Dubovsky et al., J Immunother 30:675-683 (2007), incorporated by reference herein as if set forth in its entirety. Briefly, panels of 128 lambda phage encoding unique prostate-associated antigens were assembled (Table I). Phage included those antigens initially identified in individuals with prostate cancer or chronic prostatitis by SEREX (Dunphy et al., 2004 supra; Dunphy et al., 2005, supra; Morse and McNeel, 2010 supra; Hoeppner et al., 2006 supra), or were constructed to express specific genes of interest based on prior studies (Dubovsky et al., 2007 supra; Olson and McNeel, Prostate 67:1729-1739 (2007) incorporated herein by reference as if set forth in its entirety). The following antigens were included in the panel: 29 cancer-testis antigens (CTA), 41 antigens identified in individuals with chronic prostatitis (PRO), 28 antigens identified in individuals treated with androgen deprivation (ADT), and 30 antigens identified in individuals treated with other therapies (PCA).

100,000 pfu lambda phage each carrying a gene that encodes one of the 128 antigens of the panel were robotically spotted in triplicate in a 16×24 array onto lawns of E. coli (XL-1 blue strain) growing in agar-containing OmniTray plates. Replicates for individual antigens were staggered in position across the array to account for regional variation on individual filters. For initial studies, phage encoding human immunoglobulin G (IgG) were included as a positive control and empty phage constructs were similarly included as a negative control. Plates were allowed to dry at room temperature for 20 minutes and incubated at 37° C. for 4 hours after which nitrocellulose membranes suffused with 10-mM isopropyl β-D-thiogalactopyranoside (IPTG) (Fisher Scientific, Pittsburgh, Pa.) were overlaid. Plates were incubated at 37° C. overnight to allow for recombinant expression of the antigen encoded by the protein. After 16-20 hours, membranes were removed, washed twice in TBST (50 mM Tris pH 7.2, 100 mM NaCl, 0.5% Tween-20) for 10 minutes and once in TBS (50 mM Tris pH 7.2, 100 mM NaCl) for an additional 10 minutes. Membranes were blocked in blocking solution (TBST+1% BSA), and incubated at 4° C. with human sera (diluted 1:100 in blocking solution) overnight. Membranes were washed the following day and blocked prior to incubation with a mouse anti-human IgG antibody conjugated to alkaline phosphatase (Sigma, St. Louis, Mo.) to detect human IgG. Membranes were washed again and incubated in 0.3 mg/mL nitro blue tetrazolium chloride (NBT) (Fisher Scientific) and 0.15 mg/mL 5-bromo 4-chloro 3-indoylphosphate (BCIP) (Fisher Scientific) in 100-mM Tris 9.5, 100-mM NaCl, and 5-mM MgCl2 to detect immunoreactivity. Membranes were washed with large volumes of deionized water and dried at room temperature prior to evaluation.

Membranes were scanned using a color image scanner and the digital format aligned with a 16×24 grid using densitometry software (ImageQuant TL, Amersham Biosciences, GE Healthcare Life Sciences, Piscataway, N.J.). For initial studies, immunoreactivity was quantified by measuring the density at each spot; values of replicates for individual antigens were averaged. Background correction was then made by subtracting the average of empty phage construct replicate densities on individual membrane and normalized by dividing by the average of IgG positive control replicate densities on each membrane. Transformation of densitometry data resulted in density values for individual antigens relative to a negative control and a positive control (set at 0.0 and 1.0 respectively). For subsequent studies, immunoreactivity was judged as “positive” or “negative” by visual inspection, as previously described (Dunphy et al., J. Clin. Immunol. 24:492-501 (2004), incorporated herein by reference as if set forth in its entirety; Dubovsky et al., 2007 supra). Briefly, four independent individuals looked at each membrane and scored individual spots as immunoreactive or not reactive by visually comparing each spot to a negative control. Antigens for which 0-1 of replicates determined immunoreactive with individual sera were defined as negative for immunoreactivity, and for which 2-3 of the replicates determined immunoreactive were defined as positive.

TABLE I One embodiment of the antigen panel. Des- SEQ igna- GenBank ID tion Accession NO: Gene name PRO1 NM_006423.1 1 Rab acceptor PRO2 NM_007124.1 2 U-trophon PRO3 NM_000484.1 3 Amyloid Beta (4) precursor protein PRO4 NM_002709.1 4 Protein Phosphatase 1 PRO5 AC005822.1 5 hRPK.209-J-20 DNA from chromosome 17 PRO6 AF308301.1/ 6 NY-BR-87/Ribosomal protein S26 NM_030811.2 PRO7 NM_014761.1 7 KIAA0174 from chromosome 16 PRO8 AF273042.1 8 Cutaneous T cell lymphoma tumor antigen sel-1 PRO9 AK096728.1 9 FLJ39409 Cdna PRO10 NM_001747.1 10 Macrophage capping protein gelsolin-like (CAPG) PRO11 NM_000717.2 11 Carbonic anhydrase IV PRO12 AL136040.5 12 BAC C-2506P8 from chromosome 14 PRO13 AC084864.4 13 RP11-738B7 DNA from chromo- some 7 PRO14 NM_001813.1 14 Centromere protein E PRO15 M27274.1 15 Prostate specific antigen (PSA) PRO16 NM_012116.2 16 Cas-Br-M ecotropic retroviral transforming sequence c (CBLC) PRO17 BC006286.1 17 Dual specificity phosphatase 12 PRO18 NM_144767.1/ 18 Protein kinase A anchor protein 13/ BC017368.1/ lymphoid blast crisis oncogene/ AF126008.1 breast cancer nuclear receptor- binding auxiliary protein (BRX) PRO19 AC073879.7 19 BAC RP11-752K22 from chromo- some 2 PRO20 AB017363.1 20 Frizzled-1 PRO21 AL365273.25 21 RP11-429G19 DNA from chromo- some 10 PRO22 XM_047011.2 22 o-fucosyltansferase PRO23 NM_017582.3 23 NICE5 PRO24 NM_014190.1 24 Adducin 1 PRO25 AL138752.5 25 RP11-3J10 on chromosome 9 PRO26 BC024007.1 26 Chitobiase PRO27 AK001572.1 27 FLJ10710 cDNA PRO28 AL356915.19 28 RP11-3J10 on chromosome 13 PRO29 NM_006117.1/ 29 Peroxisomal D3, D2 enoyl CoA AF257175.1 isomerase/Hepatocellular carci- noma associated antigen 64 PRO30 XM_033511.8 30 Helicase with SNF2 domain PRO31 AF039689.1/ 31 NY-CO-7/STUB1/CLL-associated XM_083939.1/ antigen KW-8 AF432221.1 PRO32 AC021558.10 32 RP11-746L20 DNA from chromo- some 8 PRO33 NM_031946.2 33 Centaurin gamma 3 PRO34 BC034250.1 34 Pituitary tumor-transforming 1 interacting protein PRO35 AC069506.14 35 BAC RP11-321G3 PRO36 AC011489.6 36 CTB-179K24 DNA on chromo- some 19 PRO37 NM_032415.2 37 Caspase domain recruitment (CARD11) PRO38 NM_003379.3 38 Cytovillin 2 PRO39 BC029529.1 39 Beta tubulin PRO40 L07872.1 40 Recombination signal binding protein (RBPJK) PRO41 NM_006455.1 41 Nucleolar autoantigen/MAD-Pro- 34 CTA1 NM_004988 42 Mage A1 CTA2 BC007343 43 SSX-2 CTA3 AJ003149 44 Ny-ESO1 CTA4 NM_021123 45 Gage 7 CTA5 U90841 46 SSX-4 CTA6 BC015020 47 NXF-2 CTA7 BC022011 48 TPX 1 CTA8 BC009538 49 Xage 1 CTA9 BC002833 50 Lage 1 CTA10 BC010897 51 Page 1 CTA11 BC081566 52 Mage E1 CTA12 BC054023 53 Span XC CTA13 BC064547 54 Adam 2 CTA14 BC037775 55 TSP 50 CTA15 BC034320 56 NY-SAR 35 CTA16 BC022064 57 Fate 1 CTA17 BC009230 58 Page 5 CTA18 BC023635 59 Lip1 CTA19 BC032457 60 SPA17 CTA20 BE387798 61 Mage A8 CTA21 BE897525 62 Mage B1 CTA22 BC026071 63 Mage B2 CTA23 BC017723 64 Mage A4 CTA24 BC001003 65 SSX-1 CTA25 BC069397 66 Gage 2 CTA26 BC069470 67 Gage 4 CTA27 BC016803 68 Mage A3 CTA28 NM_002762 69 MAD-CT-1 CTA29 AK097414 70 MAD-CT-2 PCA1 NM_025161.4 71 Chromosome 17 gene contig. PCA2 NM_000972.2 72 Ribosomal protein L7a PCA3 NM_152636.2 73 Chromosome 12 gene contig. PCA4 NM_001134194.1 74 Prostatic acid phosphatase PCA5 NM_003291.2 75 Tripeptidyl peptidase II PCA6 NM_006690.3 76 Matrix metallopeptidase 24 PCA7 NM_000990.4 77 Ribosomal protein L27a PCA8 NM_002652.2 78 Prolactin-induced protein PCA9 NM_005349.2 79 Immunoglobulin Kappa J region PCA10 NM_005817.2 80 Mannose-6-phosphate receptor binding protein 1 PCA11 NM_013267.2 81 Glutaminase 2 PCA12 NM_018979.2 82 WNK lysine deficient protein kinase 1 PCA13 NM_020718.3 83 Ubiquitin specific peptidase 31 PCA14 NM_003007.2 84 Semenogelin I, transcript variant 1 PCA15 NM_022735.3 85 Acyl-coenzyme A binding domain containing 3 PCA16 NM_001040284.1 86 PAP associated domain PCA17 NM_020187.2 87 Chromosome 3 gene contig. PCA18 NM_002712.1 88 Protein phosphatase 3, regulatory subunit 7 PCA19 NM_014220.2 89 Transmembrane 4 L6 family mem- ber 1 PCA20 NM_001135592.1 90 Ribosomal protein S27a PCA21 NM_012401.2 91 Plexin B2 PCA22 NM_000985.3 92 Ribosomal protein L17 PCA23 NM_080608.3 93 Chromosome 20 gene contig. PCA24 NM_005165.2 94 Aldolase C PCA25 NM_000969.3 95 Ribosomal protein L5 PCA26 NM_001958.2 96 Eukaryotic translation elongation factor 1 alpha 1 PCA27 NM_025108.2 97 Chromosome 16 gene contig. PCA28 NM_015358.2 98 Zinc-finger protein, CW type with coiled-coil domain 3 PCA29 NM_001130410.1 99 Acetyl-coenzyme A acyltransfer- ase 1 PCA30 NM_000044.2 100 Androgen receptor ligand-binding domain ADT1 NM_004759.3 101 Mitogen-activated protein kinase- activated protein kinase 2 ADT2 NM_001103.2 102 Actinin alpha 2 ADT3 NM_002518.3 103 Neuronal PAS domain protein 2 (NPAS2) ADT4 NM_033138.2 104 Caldesmon 1 (CALD1) ADT5 NM_001459.2 105 fms-related tyrosine kinase 3 ligand ADT6 NM_022474.2 106 Membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5) ADT7 NM_006022.2 107 TSC22 domain family, member 1 (TSC22D1) ADT8 NM_001001522.1 108 Transgelin ADT9 NM_022758.4 109 Chromosome 6 gene contig ADT10 NM_002695.3 110 polymerase (RNA) II (DNA directed) polypeptide E (POLR2E) ADT11 NM_001018160.1 111 NEDD8 activating enzyme subunit 1 (NAE1) ADT12 NM_015313.1 112 Rho guanine nucleotide exchange factor 12 (ARHGEF12) ADT13 NM_152374.1 113 Chromosome 1 gene contig ADT14 NM_001100873.1 114 Chromosome 16 gene contig ADT15 NM_001136204.1 115 Regulator of chromosome conden- sation 2 (RCC2) ADT16 NT_006713.15 116 Chromosome 5 gene contig (splicing factor, arginine/serine- rich 12) ADT17 NM_025157.3 117 Paxillin (PXN) ADT18 NM_016143.2 118 NSFL1 (p97) cofactor (p47) NSFL1C ADT19 NM_004913.2 119 Chromosome 16 gene contig ADT20 NM_207356.2 120 Chromosome 1 gene contig ADT21 NM_003104.4 121 Sorbitol dehydrogenase (SORD) ADT22 NT_006316.16 122 Chromosome 4 gene contig (solute carrier family 2, facilitated glucose transporter) ADT23 NM_013336.3 123 Sec 61 alpha 1 subunit ADT24 NM_002474.2 124 Myosin heavy chain 11 (MYH11) ADT25 NR_002819.2 125 Metastasis associated lung adenocarcinoma transcript 1 (MALAT1) ADT26 NM_001012321.1 126 Similar to lamanin receptor 1 (ribosomal protein SA (RPSA), from chromosome 19) ADT27 NT_009952.14 127 Chromosome 13 gene contig (heparan-sulfate 6-O-sulfotrans- ferase 3) ADT28 NM_021239.2 128 RNA binding motif protein 25 (RBM 25)

Statistical Analyses:

Data collected from preliminary studies analyzing individuals with castrate-resistant prostate cancer and normal male blood donors were plotted as relative density values representing detection of antibodies specific to 125 prostate cancer-associated antigens for individual individuals. Median relative density values for individual antigens were calculated in both castrate-resistant prostate cancer samples and normal control samples and the non-parametric Wilcoxon Rank Sum test was used to compare the medians of the two groups. The Benjamini-Hochberg False-Discovery Rate (FDR) method for multiple testing was used to control the type I error (Benjamini et al., J. Roy. Stat. Soc. B (Method) 57:289-300 (1995) incorporated by reference herein as if set forth in its entirety). The frequencies of IgG responses were compared between populations using Fisher's exact test. Receiver Operating Curve (ROC) analysis was performed to identify a subset of prostate cancer-associated antigens with the highest predictive value for detecting prostate cancer cases when compared to normal controls. The positive likelihood ratio value was used to quantify the predictive value for individual markers. The proportions of individuals with at least one positive IgG response and the proportions of individuals with at least three positive IgG responses in the subset of predictive markers were compared between populations by performing logistic regression analysis where population groups were included as factors. Dunnett's multiple testing procedure was used to compare the proportions between the individual populations and the control (normal) group. All p-values are two-sided, with p<0.05 indicating statistically significant differences. The data analysis was performed using SAS® version 9.2 software (SAS Corp., Cary, N.C.).

Individual Populations:

Sera were obtained from individuals with chronic prostatitis (n=45, median age 42, age range 19-62), prostate cancer (n=151, median age 67, age range 44-86), and men without a history of known prostate disease (n=78, median age 32, age range 18-62). Among the individuals with prostate cancer, 18 were collected from individuals at the time of diagnosis prior to definitive radiation treatment or prostatectomy (pretreatment), 32 were collected from individuals after definitive treatment without evidence of disease recurrence (limited stage), 44 were collected from individuals with metastatic disease recurrence on androgen deprivation therapy (androgen-dependent), and 57 were collected from individuals with castrate-resistant, metastatic disease. Sera were also obtained from male individuals with other cancers (melanoma, n=4; renal, n=17; testicular, n=5; other, n=5; median age 58, age range 30-74) for use as controls. All subjects gave written Institutional Review Board-approved consent for the use of their blood for immunological studies. Blood was collected at the University of Wisconsin-Madison Hospital and Clinics (Madison, Wis.) or at the University of Washington Medical Center (Seattle, Wash.), and sera were stored in aliquots at −20° C. to −80° C. until used for analysis.

Results

Individuals with Prostate Cancer have Higher Frequencies of Detectable Antibodies Specific for Prostate Cancer-Associated Antigens than Men without Cancer.

To determine if specific antigens are commonly recognized in the sera of individuals with prostate cancer, and if a particular set of antigens is more frequently recognized than other antigen sets, phage encoding 125 unique, prostate cancer-associated antigens obtained from prior studies (Table I) were spotted in replicate onto bacterial lawns, transferred to nitrocellulose membranes, and probed with individual sera samples, as illustrated in FIG. 1. IgG specific for phage-encoded plaques were detected using a mouse anti-human IgG antibody, immunoreactivity was quantified by densitometry, and then normalized to internal controls (0=reactivity equivalent to phage not encoding a protein; 1=reactivity equivalent to phage encoding human IgG). Immunoreactivity to multiple antigens was detected in the individual population sampled (i.e., individuals with castrate-resistant metastatic prostate cancer) that was absent in the sera of 25 healthy male blood donors (FIG. 2A-H). Of the 125 antigens evaluated, median antibody responses to 27 (22%) antigens were significantly higher in the sera of individuals with prostate cancer compared with controls (p<0.05, Wilcoxon Rank Sum test, FIG. 2A-H). Of these 27 antigens, 22 were previously identified in individuals with chronic prostatitis.

Antibody Responses to Antigens of the Antigen Panel are Evident in Individuals with Early and Late Stages of Prostate Cancer and in Individuals with Prostatitis.

To determine if recognition of particular antigens distinguishes individuals with prostate cancer from individuals with prostatitis or from men without known prostate disease, sera from a larger population of healthy male control blood donors (n=53), individuals with chronic prostatitis (n=45), and individuals with different stages of prostate cancer (n=126) were analyzed. Serum samples were obtained from men with newly diagnosed prostate cancer (pre-treatment, n=18), individuals with treated disease and no evidence of recurrence (n=32), individuals with metastatic disease responsive to androgen deprivation therapy (n=44), and additional individuals with castrate-resistant metastatic disease (n=32). In addition, the panel of antigens was modified to exclude two antigens (Pro39 and ADT28) not immunologically recognized in the initial screen, and to include phage containing genes that encoded three additional antigens (Mad-Pro-30, SEQ ID NO: 30; Mad-Pro-34, SEQ ID NO: 34; and the androgen receptor ligand-binding domain, SEQ ID NO:129) that had previously been identified as immunologically recognized antigens (Dunphy et al., 2004 supra; Olson and McNeel, 2007 supra). To account for background reactivity of individual membranes and variability in plaque immunoreactivity, each of the replicate individual plaques was visually scored as immunoreactive or not.

As demonstrated in FIG. 3A, immunoreactivity to multiple antigens was identified. FIG. 3A shows a heatmap depicting relative immunoreactivity for each antigen, grouped by the study from which the antigens were originally identified, and for each individual or control group. Spots are graded in color intensity from 3 of 3 replicates visually immunoreactive (white), to 2 of 3 (grey), to not immunoreactive (black). Overall, however, responses to at least one antigen were not more frequently observed in the individual population (72/126, 57%) or prostatitis population (28/45, 62%) compared with the control population (22/53, 42%; p=0.11 and p=0.08, respectively). We identified no single antigen to which immunoreactivity was significantly more frequent in the individual population than in the control population. Instead, 23 antigens with high (>4) positive likelihood ratio values were identified based on a ROC analysis of IgG responses to antigens among prostate cancer individual samples compared to control individual samples (Table II). FIG. 3B-F shows a subset analysis for the 23 antigens with the highest positive likelihood ratio values when comparing prostate cancer cases to normal control cases.

TABLE II One embodiment of the antigen panel. Shown is the subset of lambda phage-encoded antigens with the highest specificity for prostate cancer based on receiver operating curve analysis (see also FIG. 3B-F). Antigens with a positive likelihood ratio > 4 (sensitivity/(1-specificity)) are included, and the positive likelihood ratio is shown. Positive Des- Likeli- SEQ igna- hood ID tion Ratio NO: Gene name ADT14 ∞ 114 Chromosome 16 gene contig CTA3 ∞ 44 NY-ESO-1 CTA23 ∞ 64 Mage A4 PCA6 ∞ 76 Matrix metallopeptidase 24 PCA 8 ∞ 78 Prolactin-induced protein PCA 10 ∞ 80 Mannose-6-phosphate receptor binding protein 1 PCA 16 ∞ 86 PAP-associated domain PRO5 ∞ 5 hRPK.209-J-20 DNA from chromosome 17 PRO 10 ∞ 10 Macrophage capping protein gelsolin-like (CAPG) PRO 12 ∞ 12 BAC C-2506P8 from chromosome 14 PRO 17 ∞ 17 Dual specificity phosphatase 12 PRO 18 ∞ 18 Protein kinase A anchor protein 13/lymphoid blast crisis oncogene/breast cancer nuclear receptor-binding auxiliary protein (BRX) PRO 19 ∞ 19 BAC RP11-752K22 from chromosome 2 PRO 20 ∞ 20 Frizzled-1 PRO 24 ∞ 24 Adducin 1 PRO 25 ∞ 25 RP11-3J10 on chromosome 9 PRO 35 ∞ 35 BAC RP11-321G3 CTA27 8.4 68 Mage A3 PCA 21 8.4 91 Plexin B2 PRO 40 6.7 40 Recombination signal binding protein (RBPJK) PCA 2 5.5 72 Ribosomal protein L7a PRO 34 5.4 34 Pituitary tumor-transforming 1 interacting protein PRO 32 4.2 32 RP11-746L20 DNA from chromosome 8

Antibody Responses to Prostate Tissue-Associated Antigens Occur Irrespective of the Stage of Prostate Cancer.

FIG. 4 shows the proportion and standard error of subjects in each population recognizing at least one (FIG. 4A) or at least three (FIG. 4B) of the antigens identified in Table II. Asterisks denote higher frequency compared to the control population (p<0.05, computed by logistic regression analysis and Dunnett's method for multiple comparisons). A subset analysis showed that the proportion of individuals with a detectable antibody response to at least one of the 23 antigens was significantly higher in the prostate cancer individual population when compared to the control population (FIG. 4A), that is, 48/126 (38%) versus 3/53 (6%) (p<0.001). Antibody responses detected in sera from prostatitis individuals (15/45, 33%) were significantly higher than those detected in the control population (p=0.003). Antibody responses detected in sera from prostatitis individuals were not significantly different from those detected in the prostate cancer individual population (FIG. 4A). As shown in FIG. 4B, the presence of immunoreactivity to three or more of the 23 antigens was more frequent in individuals with prostate cancer (12/126, 10%) and individuals with prostatitis (4/45, 9%) relative to male control blood donors (1/53, 2%).

Antibody Responses to Prostate-Associated Antigens are Uncommon in Sera from Male Individuals with Non Prostate Malignancies.

The majority of antigens recognized by prostate cancer and prostatitis individuals are not prostate-specific in terms of expression, suggesting that the responses detected could be signatures of non-prostate-specific inflammatory conditions. To test this possibility, antibody responses to a panel of 126 antigens were evaluated using sera obtained from male individuals (n=31) with other non-prostate cancers (renal cell cancer, n=17; testicular cancer, n=5; melanoma, n=4; head and neck cancer, n=1; GI stromal tumor, n=1; bladder cancer, n=1; non-small cell lung cancer, n=1; carcinoid tumor n=1). FIG. 5 shows a heatmap depicting immunoreactivity for each antigen, grouped by the study from which they were originally identified, and for each individual tumor type. Spots were scored positive (white) if visually immunoreactive in at least 2 of 3 replicates. As shown in FIG. 5, while antibody responses were detectable to at least one of the 126 antigens in 7/31 sera samples (23%), only one response in 1/31 sera samples (3%) was detected to one of the 23 prioritized antigens. This result was not statistically different in frequency from responses identified in the non-cancer control population. The one response identified was to the Pro32 antigen, which exhibited the lowest positive likelihood ratio (Table II).

Discussion

Antigenic Targets of a Prostate-Associated Immune Response are Recognized in Populations of Individuals with Prostatitis and Prostate Cancer.

Immune responses to antigens originally identified in individuals with chronic prostatitis are also recognized in individuals with advanced prostate cancer relative to controls, suggesting that many “prostatitis antigens” represent true immunologically recognized antigens of the prostate, many of which coincide with antibody recognition in individuals with prostate cancer. Specific antibody responses to at least one member of a subset of 23 of these antigens were detectable in sera of individuals with prostate cancer or clinical prostatitis, but were rare in sera from male subjects with other types of cancer and in male subjects without prostate cancer or prostatitis.

These results, while not suggesting causality, suggest an association between chronic inflammatory conditions, such as prostatitis, and prostate cancer, or at least suggest that targets of a prostate-associated immune response can be recognized in these disorders. These results further suggest that the prostate expresses a set of antigens recognized immunologically by multiple individuals. The evaluation of antibody responses to prostate-associated antigens can potentially identify individuals in a premalignant inflammatory state at risk for developing prostate cancer. To further test this potential, sera obtained from individuals without a history of prostatitis but who developed prostate cancer within several years can be screened using the set of antigens identified herein.

Advantages of the phage immunoblot approach described here are the ease of transfection and protein expression in bacteria, particularly for novel proteins for which there are no available reagents, and the ability to simultaneously evaluate antibody responses to multiple antigens simultaneously from a single sample.

It is understood that certain adaptations of the invention described in this disclosure are a matter of routine optimization for those skilled in the art, and can be implemented without departing from the spirit of the invention, or the scope of the appended claims. All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. It is understood, however, that examples and embodiments of the present invention set forth above are illustrative and not intended to confine the invention. The invention embraces all modified forms of the examples and embodiments as come with the scope of the following claims.

Claims

1. An antigen panel for identifying immunoreactivity associated with a premalignant or malignant prostate, the panel comprising antigens encoded by SEQ ID NO:5, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:40, SEQ ID NO:44, SEQ ID NO:64, SEQ ID NO:68, SEQ ID NO:72, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:86, and SEQ ID NO:91, the encoded antigens being immobilized on one of a membrane, a plate, and a filter, and having a positive likelihood ratio of at least 4.

2. The panel of claim 1, wherein the panel further comprises an antigen encoded by a nucleic acid having a sequence selected from the group consisting of SEQ ID Nos: 1-4, 6-9, 11, 13-16, 21-23, 26-31, 33, 36-39, 31-43, 45-63, 65-67, 69-71, 73-75, 77, 79, 81-85, 87-90, and 92-128.

3. The panel of claim 1, the panel consisting of antigens encoded by SEQ ID NO:5, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:40, SEQ ID NO:44, SEQ ID NO:64, SEQ ID NO:68, SEQ ID NO:72, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:86, and SEQ ID NO:91.

4. The panel of claim 1, wherein at least three of the antigens in the panel elicit an immune response in at least about 9% of individuals with prostatitis or prostate cancer.

5. The panel of claim 1, wherein each antigen is expressed by a phage and attached to the membrane, plate or filter via the phage.

6. The panel of claim 1, wherein the plate is a multi-well plate.

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Patent History
Patent number: 10191056
Type: Grant
Filed: Dec 23, 2015
Date of Patent: Jan 29, 2019
Patent Publication Number: 20160238606
Assignee: Wisconsin Alumni Research Foundation (Madison, WI)
Inventors: Douglas G. McNeel (Madison, WI), Brett B. Maricque (Green Bay, WI)
Primary Examiner: Peter J Reddig
Application Number: 14/757,607
Classifications
Current U.S. Class: Assay In Which A Label Present Is An Enzyme Substrate Or Substrate Analogue (435/7.72)
International Classification: C40B 40/10 (20060101); G01N 33/574 (20060101); G01N 33/531 (20060101);